In 1824 Pope Leo XII restored the order and returned to the Jesuits what became the Pontifical Gregorian University, but allowed the secular clergy who had been replaced to continue to devote themselves to teaching: at the site where the Palace of Saint Apollinaris stood in 1853, Pope Pius IX founded the Faculty of Canon Law and Civil Law and the Pontifical Institute Utriusque Iuris. The new institution took the name of Pontifical Roman Seminary University.

According to the Decree of the Ministry of University and Scientific Research of the Italian Republic of 21 September 2006, implementing Law No. 63, March 5, 2004, the Laurea in Law (L/31) and Laurea Magistrale in Law (LMG/01) are equivalent to degrees issued by Italian universities.

The Grand Chancellor is, under the statutes of the University, the vicar general of His Holiness for the Diocese of Rome, who was Cardinal Agostino Vallini from 2008 to 2017. The rector is Bishop Enrico dal Covolo, a theologian.

The library of the Pontifical Lateran University - "Library of Blessed Pius IX", known originally as the "Biblioteca Pia" - was founded by Pope Pius IX in 1854. The history of the library is connected directly to the foundation of the university at its original seat at St. Apollinare in Rome. The library is in fact a collection of smaller libraries from various ecclesial and academic institutes in Rome which have been amalgamated to form the present library. The library consists of collections from the private libraries of Pope Gregory XIII, Pope Pius IX, Pope Pius XII, the German College,the monastery of SS. Bonifacio and Alessio on the Aventine, and the library of the Geronimiani fathers. Successively various ex-alumni have contributed to the library.
A new building for the housing of the library and reading room was built and officially inaugurated by Pope Benedict XVI on 21 October 2007.
As of 2014[update] the library had some 600,000 books and a collection of 40,000 rare and antique volumes.

The University is linked to university Pastoral Institute Redemptor Hominis and the Theological Institute of Assisi.
The Theological Institute of Assisi is a training college established in 1971 in Assisi in the structures of Saint Francis sharing the premises of the Sacred Convent with the community of Friars Minor Conventual.
The Institute also has a documentation center. Since 1993, it is attached to the Faculty of Theology at the Pontifical University Lateran, and serves as the academic institution designed to train students in theology. It organizes courses of studies leading to diplomas of Bachelor of Sacred Theology and Licentiate of Sacred Theology, and Franciscan studies for those wishing to be recruited into church office or intending to teach the Catholic religion in schools.